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Iodine in PDB 4p4v: Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk

Protein crystallography data

The structure of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk, PDB code: 4p4v was solved by R.K.Spencer, J.S.Nowick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.30 / 1.97
Space group P 42 2 2
Cell size a, b, c (Å), α, β, γ (°) 62.030, 62.030, 44.676, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 22.2

Other elements in 4p4v:

The structure of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk (pdb code 4p4v). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk, PDB code: 4p4v:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 4p4v

Go back to Iodine Binding Sites List in 4p4v
Iodine binding site 1 out of 3 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I5

b:40.2
occ:1.00
I A:PHI5 0.0 40.2 1.0
CZ A:PHI5 2.1 57.2 1.0
CE1 A:PHI5 3.0 57.1 1.0
CE2 A:PHI5 3.1 61.2 1.0
HE1 A:PHI5 3.1 68.5 1.0
HE2 A:PHI5 3.1 73.5 1.0
HB2 C:LEU3 3.5 55.2 1.0
O C:LEU3 3.5 31.5 1.0
H C:PHI5 3.6 41.6 1.0
HD2 C:PHI5 3.7 61.7 1.0
HA C:LEU4 3.8 46.4 0.6
HA C:LEU4 3.8 46.4 0.4
CD2 C:PHI5 3.9 51.4 1.0
C C:LEU3 3.9 34.1 1.0
HB2 C:PHI5 4.0 65.3 1.0
N C:PHI5 4.0 34.6 1.0
CG C:PHI5 4.2 52.6 1.0
HB3 C:LEU3 4.2 55.2 1.0
N C:LEU4 4.2 34.8 0.6
N C:LEU4 4.2 35.8 0.4
CA C:LEU4 4.3 38.6 0.6
CB C:LEU3 4.3 46.0 1.0
CA C:LEU4 4.3 38.6 0.4
C C:LEU4 4.3 38.0 0.6
C C:LEU4 4.3 38.0 0.4
CD1 A:PHI5 4.3 51.6 1.0
CE2 C:PHI5 4.3 44.1 1.0
CD2 A:PHI5 4.4 58.7 1.0
CB C:PHI5 4.5 54.4 1.0
HE2 C:PHI5 4.5 52.9 1.0
HB2 A:MAA13 4.7 53.7 1.0
H C:LEU4 4.8 41.7 0.6
H C:LEU4 4.8 43.0 0.4
CA C:LEU3 4.8 33.9 1.0
CA C:PHI5 4.9 34.2 1.0
CG A:PHI5 4.9 45.0 1.0
HD12 C:LEU3 4.9 99.1 1.0
CD1 C:PHI5 5.0 56.4 1.0

Iodine binding site 2 out of 3 in 4p4v

Go back to Iodine Binding Sites List in 4p4v
Iodine binding site 2 out of 3 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I5

b:38.3
occ:1.00
I B:PHI5 0.0 38.3 1.0
CZ B:PHI5 2.1 45.3 1.0
CE1 B:PHI5 3.1 51.1 1.0
CE2 B:PHI5 3.1 55.0 1.0
HE1 B:PHI5 3.1 61.3 1.0
HE2 B:PHI5 3.1 66.0 1.0
CD1 B:PHI5 4.3 55.7 1.0
CD2 B:PHI5 4.4 57.1 1.0
HB2 B:MAA13 4.7 49.5 1.0
CG B:PHI5 4.9 46.6 1.0

Iodine binding site 3 out of 3 in 4p4v

Go back to Iodine Binding Sites List in 4p4v
Iodine binding site 3 out of 3 in the Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Hexamer Formed By A Macrocyclic Peptide Derived From Beta-2- Microglobulin (63-69) - (Orn)Yll(Phi)Yte(Orn)Kva(Maa)Avk within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I5

b:38.4
occ:1.00
I C:PHI5 0.0 38.4 1.0
CZ C:PHI5 2.1 41.5 1.0
CE1 C:PHI5 3.1 51.7 1.0
CE2 C:PHI5 3.1 44.1 1.0
HE1 C:PHI5 3.1 62.1 1.0
HE2 C:PHI5 3.1 52.9 1.0
HA B:TYR6 3.3 40.0 1.0
HG22 B:THR7 3.3 42.7 1.0
HB3 B:PHI5 3.5 38.4 1.0
O A:LEU3 3.5 35.9 1.0
HB2 A:LEU3 3.5 38.0 1.0
O B:PHI5 3.6 30.9 1.0
HG13 B:VAL11 3.6 45.9 1.0
H A:PHI5 3.8 35.1 1.0
HA A:LEU4 3.8 45.3 0.3
HA A:LEU4 3.8 45.6 0.7
C B:PHI5 3.9 29.9 1.0
C A:LEU3 3.9 32.5 1.0
CA B:TYR6 4.0 33.3 1.0
HD2 A:PHI5 4.0 70.4 1.0
HB2 B:PHI5 4.0 38.4 1.0
CD2 A:PHI5 4.0 58.7 1.0
HB2 A:PHI5 4.1 42.3 1.0
N B:TYR6 4.1 31.6 1.0
N A:PHI5 4.1 29.2 1.0
HG22 B:VAL11 4.1 61.0 1.0
CB B:PHI5 4.1 32.0 1.0
N A:LEU4 4.2 35.5 0.7
H B:THR7 4.2 43.1 1.0
CG2 B:THR7 4.2 35.6 1.0
N A:LEU4 4.2 35.8 0.3
C B:TYR6 4.3 33.6 1.0
CG A:PHI5 4.3 45.0 1.0
HB3 A:LEU3 4.3 38.0 1.0
CB A:LEU3 4.3 31.7 1.0
CA A:LEU4 4.3 37.8 0.3
CA A:LEU4 4.3 38.0 0.7
N B:THR7 4.3 35.9 1.0
HG11 B:VAL11 4.3 45.9 1.0
HG21 B:THR7 4.3 42.7 1.0
C A:LEU4 4.3 34.5 0.3
C A:LEU4 4.3 34.5 0.7
HB B:THR7 4.3 47.3 1.0
CD1 C:PHI5 4.3 56.4 1.0
CD2 C:PHI5 4.4 51.4 1.0
CG1 B:VAL11 4.4 38.3 1.0
CE2 A:PHI5 4.5 61.2 1.0
CB A:PHI5 4.6 35.2 1.0
H B:TYR6 4.6 38.0 1.0
H A:LEU4 4.6 42.7 0.7
HB2 C:MAA13 4.7 44.6 1.0
CA B:PHI5 4.7 27.5 1.0
HG21 B:VAL11 4.7 61.0 1.0
H A:LEU4 4.7 43.0 0.3
CA A:LEU3 4.7 29.2 1.0
HE2 A:PHI5 4.7 73.5 1.0
CB B:THR7 4.8 39.4 1.0
CG2 B:VAL11 4.8 50.8 1.0
CG C:PHI5 4.9 52.6 1.0
HG23 B:THR7 4.9 42.7 1.0
O B:TYR6 4.9 33.0 1.0
HB3 C:MAA13 4.9 44.6 1.0
CD1 A:PHI5 4.9 51.6 1.0
CA A:PHI5 4.9 29.6 1.0

Reference:

R.K.Spencer, A.G.Kreutzer, P.J.Salveson, H.Li, J.S.Nowick. X-Ray Crystallographic Structures of Oligomers of Peptides Derived From Beta 2-Microglobulin. J.Am.Chem.Soc. 2015.
ISSN: ESSN 1520-5126
PubMed: 25915729
DOI: 10.1021/JACS.5B01673
Page generated: Sun Dec 13 19:36:05 2020

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